In order for your site's contents to be included in the results of your custom search engine, they need to be included in the Google index. The Google index is similar to an index in a library, which lists information about all the books the library has available. However, instead of books, the Google index lists all of the webpages that Google knows about. When Google visits your site, it detects new and updated pages and updates the Google index.
To see which pages on your site are in the Google index, you can do a Google Web Search for "site:mywebsite.com".
If you want more pages included in the Google index, use the Google Search Console to submit indexing requests. These requests will change the index for both Google search and CSE search. In order for CSE to recognize the indexing request, the site or URL pattern needs to be listed in the "Sites to search section" found in the Basics tab of the Setup section in the CSE configuration. Crawling and indexing may not happen immediately.